structural biology



computational biology


Scientific degrees
2009 Professor of Biological Sciences
2005 D.habil. in biochemistry, IBB PAS, Warsaw, Poland
2001 Ph.D. in bioinformatics, Faculty of Biology, UW, Warsaw, Poland
1998 M.Sc. in microbiology, Faculty of Biology, UW, Warsaw, Poland

Professional experience – present
2002 Professor, Head of the Laboratory of Bioinformatics and Protein Engineering, IIMCB, Warsaw, Poland
2006 Visiting Professor, Faculty of Biology, AMU, Poznan, Poland

Professional experience – past
2010-2011 Deputy Director, International Institute of Molecular and Cell Biology in Warsaw (1 year rolling position)
2008 Visiting Professor, University of Tokyo, Japan (sabbatical)
2004-2006 Assistant Professor, AMU, Poznan, Poland
2002 Acting Head of the Laboratory of Bioinformatics at the IIMCB, Warsaw, Poland
2001-2002: Group Leader, Laboratory of Bioinformatics, IIMCB, Warsaw, Poland
2001 Visiting Scientist, NCBI, NLM, NIH, Bethesda, USA
1999-2001 Research Scientist, Bioinformatics Unit, IIMCB, Warsaw, Poland
1998-2000: Senior Research Assistant, Henry Ford Health System, Detroit, MI, USA

Professional affiliations – present
High Level Group of scientific advisors within the Scientific Advice Mechanism (HLG-SAM) for the European Commission (member, 11.2015-)
Polish Society for Bioinformatics, PTBI (founding member, vice-president 2007-2010, president 2011-2013)
Society of Bioinformatics in Northern Europe, SocBiN (board member, 2004-)
RNA Society (member, 2007-), International Society for Computational Biology, ISCB (member, 2001-, Senior Member 2015-)
Committee of Molecular Cell Biology, Polish Academy of Sciences (2016-2019)
Committee of Biotechnology, Polish Academy of Sciences (ex officio AMU-PAN member, 2016-2019)

Professional affiliations – past
Science Policy Committee, Polish Ministry of Science and Higher Education (member 2014-2016-2018, chairman 04-10.2015, 06-12.2016)
Council of the National Science Congress, Polish Ministry of Science and Higher Education (member, 09.2016-10.2017)
Scientific Committee of the Innovative Medicines Initiative (member, 2013-2016)
EC Advisory Group on European Research Infrastructures including e-Infrastructures, member (2013-2015)
Science Promotion Council, Polish Academy of Sciences, RUN-PAN (2013-2016)
Young Academy, Polish Academy of Sciences, AMU-PAN (2011-2016)
Science Europe, Life, Environmental and Geo Sciences (LEGS) Scientific Committee, member (2013-2015)
Committee of Evolutionary and Theoretical Biology, Polish Academy of Sciences (2008-2011, 2011-2015)
Committee of Biochemistry and Biophysics, Polish Academy of Sciences (2011-2015)

Editorial activities
Executive Editor, Nucleic Acids Research (2013-)
Series editor, Nucleic Acids and Molecular Biology (Springer Verlag, 2009-2013)
Deputy Section Editor, BMC Bioinformatics (2010-2014), Editorial Advisor (2014-)

International awards
2018 Elected as a member of Academia Europaea
2018 Elected as EMBO member
2010 ERC Starting Grant (2011-2015) – first ERC Starting Grant in biological sciences awarded for a proposal from Poland
2006 Young Researcher Award in Structural and Evolutionary Biology of the Visegrad Group Academies of Sciences
2003-2005 EMBO & HHMI Young Investigator Programme Award


Bujnicki’s research combines bioinformatics, structural biology, and synthetic biology. His scientific achievements include the development of methods for computational modeling of protein and RNA 3D structures, discovery and characterization of enzymes involved in RNA metabolism, and engineering of proteins with new functions. In the context of the EPITRAN project, it is essential to mention the development of MODOMICS, a database of RNA modification pathways, and experimental as well as theoretical studies on RNA modification enzymes, in particular RNA methyltransferases.


1. Smietanski M, Werner M, Purta E, Kaminska KH, Stepinski J, Darzynkiewicz E, Nowotny M, Bujnicki JM. Structural analysis of human 2-O-ribose methyltransferases involved in mRNA cap structure formation. Nature Commun 2014, 5:3004, doi:10.1038/ncomms4004. We determined the structures and the mechanisms of actions of CMTr1 and CMTr2, using X-ray crystallography in combination with computational modeling. Our results revealed how the human methyltransferases recognize and chemically modify the cap structure and that they do it differently from viral enzymes, thereby providing a framework for targeting these viral proteins by drugs that are safe for humans.
2. Boccaletto P, Machnicka MA, Purta E, Piatkowski P, Baginski B, Wirecki TK, de Crécy-Lagard V, Ross R, Limbach PA, Kotter A, Helm, Bujnicki JM. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 2018 Jan 4;46(D1):D303-D307 MODOMICS is a database system that stores information about RNA modification pathways, enzymes involved, and sequences of RNA molecules containing modified residues. It is very popular in the RNA modification community, it has been periodically updated and the updates have been published in a series of articles, which together have been cited  >700 times.
3. Rother M, Rother K, Puton T, Bujnicki JM, ModeRNA: A tool for comparative modeling of RNA 3D structure, Nucleic Acids Res 2011 May 1;39(10):4007-22.  We developed the first fully automated method for comparative modeling of RNA 3D structures. Among unique features of ModeRNA is the ability to model not only the standard A, U, C, G, residues, but also >100 residues resulting from posttranscriptional modifications.
4 Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction Nucleic Acids Res 2016;44(7):e63. We developed a new method for the modeling of RNA 3D structures that does not require any “templates” of known structure. SimRNA has been evaluated and validated in the RNA Puzzles competition, and was found to pgenerate very accurate models.  
5. Glow D, Pianka D, Sulej A, Kozlowski L, Czarnecka J, Chojnowski G, Skowronek KJ, Bujnicki JM, Sequence-specific cleavage of dsRNA by Mini-III RNase Nucleic Acids Res 2015;43(5):2864-73. We found that RNase Mini-III from Bacillus subtilis (BsMiniIII) exhibits sequence-dependent cleavage of long dsRNA. BsMiniIII may serve as a prototype of a sequence-specific dsRNase that could possibly be used for targeted cleavage of dsRNA. The publication has been awarded the status of a Breakthrough Article.
6. Glow D, Kurkowska M, Czarnecka J, Szczepaniak K, Pianka D, Kappert V, Bujnicki JM, Skowronek KJ; Identification of protein structural elements responsible for the diversity of sequence preferences among Mini-III RNases; Sci Rep. 2016;6:38612. As a follow up of the BsMiniIII study, we analyzed 8 different MiniIII family members, demonstrated that they have different sequence preference, and successfully engineered variants with altered substrate specificities.
7. Piatkowski P, Jablonska J, Zyla A, Niedzialek D, Matelska D, Jankowska E, Walen T, Dawson WK, Bujnicki JM; SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments. Nucleic Acids Res. 2017;45(16):e150. SupeRNAlign is a new computational method for comparison of RNA 3D structures, which enables superposition with conformational changes. It performs better than other methods that enable only rigid-body comparisons and generates more accurate, biologically reasonable RNA sequence alignments.
8. Philips A, Milanowska K, Lach G, Bujnicki JM; LigandRNA: computational predictor of RNA-ligand interactions RNA 2013;19(12):1605-16. LigandRNA is a computational method for predicting the 3D structure of RNA complexed with small moleucle ligands.
9. Walen T, Chojnowski G, Gierski P, Bujnicki JM; ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes. Nucleic Acids Res. 2014;42(19):e151. ClaRNA is a new method for classyfing noncanonical interactions in RNA 3D structures .
10. Chojnowski G, Walen T, Piatkowski P, Potrzebowski W, Bujnicki JM, Brickworx builds recurrent RNA and DNA structural motifs into medium and low-resolution electron density maps. Acta Crystallogr D Biol Crystallogr 2015;71(Pt 3):697-705. RNABrickx is a new computational method for the crystallographic determination of RNA 3D structures from medium- and low-resolution electron density maps.